I'll throw my lot in with this and explain it how I'm seeing it / headcannoning it.
The Night Elves, if you've read the short story excerpt, aren't just losing Teldrassil. Their lands are being marched through, and destroyed by the Horde, their people put to the knife and annexed from their homeland for the sake of Sylvanas' war. Many demon hunters, as mentioned before in this thread, became Illidari in order to avenge their fallen loved ones, and to protect the land that remains, or to avenge the land that was lost. Asking why the Night Elf Demon Hunters decide to side with the Alliance once it is said and done is a no-brainer, it's not that they are siding with the Alliance per-say, but it's looking to avenge their people and homeland once more - and the faction of their people / method of revenge is without a doubt the Alliance, as it is where their actual race call home, and where they will turn to after the fact.
The Blood Elves on the other hand are a bit harder to predict, though the best that I can sum up is along the same lines as the Nelfs. They see the destruction, and the cost of war on other lands, and rally to their own. The Horde has lost Undercity, and though it is not inhabitable for the Alliance, what is to stop the Alliance from pushing forward north to try and claim Quel'thalas? It breeds distrust and hatred, and a want to protect what is yours. The Belfs joining the Horde would be along the same lines as the Nelfs - though looking to protect their home, rather than avenge it. Why let it happen in the first place if you can prevent it, when it's already happened everywhere else?
TL;DR: The Illidari joining factions make sense, the Nelfs to avenge their homeland, and the Belfs to protect it in time of war.
Bonus Counterargument(and Lore Tidbit): The Blood Elves were not betrayed in WC3, only Kael'thas and the forces he had on hand were thrown at an enemy, and his people followed his resentment and fell away from the Alliance over it. The Blood Elves even had to twist, warp, or even result to mind controlling their own people for the separation to happen. Don't be a sheep, the Magistrate -wants- you to believe that the Sin'dorei were betrayed, but it is far from true.
Bonus Lore: The Illidari sent out faction representatives based on race, and assigned sects of the Illidari based on the same concept. Keeping them with their people to create trust, rather than throwing a night elf into the Horde and hoping it worked out, or vice versa. There's the chance that the Illidari, when put into those situations, have created bonds or friendships, and would be reluctant to turn on their new allies or brothers in arms. You can look into the outposts in Stormwind and Orgrimmar to see that at play. It is also likely a source of controversy in the way the Illidari will pick their factions.
... LONG POST, I'M SORRY!
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